Variant report

Variant	rs9790601
Chromosome Location	chr4:103529963-103529964
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:103527709..103529974-chr4:104004958..104007042,2	MCF-7	breast:
2	chr4:103527865..103530331-chr4:103746891..103748904,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164038	Chromatin interaction
ENSG00000109332	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1005819	1.00[JPT][hapmap]
rs1020759	0.90[JPT][hapmap]
rs1020760	1.00[JPT][hapmap]
rs10489114	0.83[YRI][hapmap]
rs11722146	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11723120	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs118882	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs12509403	0.95[CEU][hapmap]
rs12509517	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12648696	0.94[CHB][hapmap]
rs1585213	0.91[JPT][hapmap]
rs1585215	0.91[JPT][hapmap]
rs1598859	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1599961	0.91[JPT][hapmap]
rs1609798	0.91[CHB][hapmap]
rs17032705	0.91[JPT][hapmap]
rs170731	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1801	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs2168805	0.86[JPT][hapmap]
rs230491	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs230492	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs230493	0.84[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs230495	0.91[JPT][hapmap]
rs230496	0.91[JPT][hapmap]
rs230498	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs230500	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs230504	0.84[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs230505	0.91[JPT][hapmap]
rs230509	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs230514	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs230515	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs230516	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs230519	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs230520	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs230521	0.91[JPT][hapmap]
rs230525	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs230526	0.91[JPT][hapmap]
rs230528	0.91[JPT][hapmap]
rs230529	0.91[JPT][hapmap]
rs230531	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs230532	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs230533	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs230534	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs230535	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs230539	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs230540	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs230541	1.00[JPT][hapmap]
rs230542	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3755867	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3774933	0.91[JPT][hapmap]
rs3774936	0.91[JPT][hapmap]
rs3774937	0.91[JPT][hapmap]
rs3774938	0.91[JPT][hapmap]
rs3774956	1.00[JPT][hapmap]
rs3774959	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3774963	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3774964	1.00[JPT][hapmap]
rs3817685	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs3821958	1.00[JPT][hapmap]
rs4235404	0.91[JPT][hapmap]
rs4648011	0.91[JPT][hapmap]
rs4648018	0.81[YRI][hapmap]
rs4648055	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4648058	1.00[JPT][hapmap]
rs4648068	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4648133	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs4698858	1.00[JPT][hapmap]
rs4698861	0.87[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap]
rs4698863	0.85[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs4699030	1.00[JPT][hapmap]
rs747559	0.91[JPT][hapmap]
rs980455	0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830020	chr4:103387343-103581284	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103483400-103541600	Weak transcription	K562	blood
2	chr4:103497600-103533400	Strong transcription	Primary B cells from peripheral blood	blood
3	chr4:103502600-103532800	Weak transcription	Brain Germinal Matrix	brain
4	chr4:103512800-103531800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr4:103513000-103542000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr4:103513200-103536200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr4:103514600-103535800	Strong transcription	Adipose Nuclei	Adipose
8	chr4:103514600-103538200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr4:103514600-103539000	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr4:103515000-103539000	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr4:103515200-103533200	Strong transcription	Primary B cells from cord blood	blood
12	chr4:103515200-103533400	Strong transcription	Primary hematopoietic stem cells	blood
13	chr4:103515200-103533600	Strong transcription	Duodenum Mucosa	Duodenum
14	chr4:103515200-103538800	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr4:103515400-103533200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:103515400-103533400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr4:103515400-103533400	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr4:103515400-103533600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr4:103515400-103538800	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr4:103515400-103538800	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr4:103515600-103533400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr4:103515600-103535600	Strong transcription	Fetal Muscle Trunk	muscle
23	chr4:103515800-103535800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr4:103515800-103538200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:103515800-103538800	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr4:103515800-103538800	Strong transcription	Rectal Smooth Muscle	rectum
27	chr4:103517600-103541600	Weak transcription	Right Atrium	heart
28	chr4:103517800-103536200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:103518400-103533200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr4:103520200-103530400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr4:103520200-103535600	Strong transcription	Left Ventricle	heart
32	chr4:103520600-103531800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr4:103520800-103538600	Strong transcription	GM12878-XiMat	blood
34	chr4:103521000-103538800	Strong transcription	Placenta	Placenta
35	chr4:103521200-103537600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr4:103521400-103532600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:103521400-103554400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:103521800-103537400	Strong transcription	HSMM	muscle
39	chr4:103522400-103535600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr4:103523200-103531600	Strong transcription	Fetal Thymus	thymus
41	chr4:103523200-103538800	Strong transcription	Liver	Liver
42	chr4:103523600-103530200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr4:103523800-103533200	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr4:103524600-103532600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
45	chr4:103524600-103533600	Strong transcription	Fetal Lung	lung
46	chr4:103524600-103538800	Strong transcription	Dnd41	blood
47	chr4:103525000-103532200	Weak transcription	Fetal Brain Male	brain
48	chr4:103525400-103530800	Strong transcription	Primary T cells from cord blood	blood
49	chr4:103525400-103537200	Strong transcription	Colon Smooth Muscle	Colon
50	chr4:103525600-103530200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links